Equestria Invaded
by ponyboycurtiss
Summary: AU Equestria is finally faced with an enemy that takes longer than two episodes to defeat. It has been two years since the war began. Our friends are scattered across Equestria. How are they dealing with the pressures of war? What will become of their friendship? Set after Season 2. Rated T for general darkness and implications of violence.
1. Chapter 1

**Equestria Invaded**

* * *

When Fluttershy finally landed after her eight-hour watch shift, her wings were droopy and her eyes were tired. Even after two years, she wasn't used to doing this much flying. Completely spent, she trotted slowly back towards the center of the encampment. Even in her tired state she couldn't help but remain alert on her way back to her small tent. If she had learned anything in the two years since the start of the war, it was to always be aware of your surroundings.

It was early evening. The sun was setting and mares were watching as their foals finished their games before returning home for the mandatory curfew. The first night watch would be starting soon. Fluttershy was glad she had finally been switched to the daytime watch. Six months of sleeping during the day and flying all night had left her feeling lonelier than ever. Not that she felt any less lonely now. But she liked feeling like she was on the same schedule as every pony else. Fluttershy was nearly to her tent when she saw that some pony was waiting for her outside the front flap. It was Big McIntosh. Fluttershy smiled weakly as she approached him.

"How are you doin'?" he asked softly.

"I'm alright. Maybe a little tired," Fluttershy replied, downplaying her exhaustion. "Are you getting ready for the nighttime patrol?"

"Yep," he said, nodding.

They stood facing each other for an inelegant moment before Big McIntosh excused himself. Fluttershy entered her tent and after removing her Guardspony's uniform, she undid the braid in her mane and the braid in her tail. The Aerial Forces were all offered the opportunity to cut their manes and tails short when they were forcibly conscripted. Those mares who wished not to do so were made to keep their hair braided at all times while on duty.

Fluttershy flopped down onto her bed and allowed her wings to spread out. They were aching terribly; it had been windier than usual. Winter was coming early that year – the Pegasi had seen to that, per the Princess' orders. It was supposed to give them an advantage.

She tried to fall asleep, but insomnia was getting the best of her. Frustrated, she sat up. It had been sweet of Big McIntosh to come say hello before he started his patrol. But every time she saw him, Fluttershy felt like crying. She tried not to stare, but his missing leg was just too obvious. He had returned home to Ponyville injured after only fourteen months of service. His back left leg had been lost in hoof to hoof combat with a patrol group of Chameleons. Big McIntosh spent the next four months in a deep depression until Ponyville was evacuated into the Evertree Forest, along with the rest of Equestria. Every pony, from Fillydelphia to Los Pegasus, was ordered to seek refuge in the ominous forest. The invading forces were too strong, and the Front Line had been pushed back too far to ensure the civilians safety any longer. Once the Ponyville settlement had settled in, the Night Watch was formed. The Watch kept a look out for anything strange in the forests. It was mostly older stallions, or injured ones, such as Big McIntosh, although there was the occasional mare as well.

Fluttershy noticed that after he had joined the Watch, Big McIntosh's outlook had improved greatly. It made her happy that he seemed to have found a purpose again. Still unable to sleep, she slipped out of her tent and went off looking for Big McIntosh. (One of the only perks of being part of the Aerial Guard was that Fluttershy was exempt from the curfew.) She thought she would join him on his patrol for a little while, and hopefully then she would feel sleepy enough that she might be able to sleep in late the next morning. It was going to be her day off, after all – the first one in three weeks.

It didn't take her too long to find him; she knew his patrol route by heart. They walked in silence, keeping their eyes on the forest at all times. Fluttershy enjoyed just being in his company. Even without his back left leg, he was so big and strong, she felt safe just having him nearby. When she started to yawn, she took it as her cue to take her leave. Fluttershy gave Big McIntosh a gentle nuzzle before heading back to her tent. Finally feeling her exhaustion catch up to her, she drifted off to sleep without any trouble.

When she finally poked her head out of her tent the next day, the sun was already high in the sky. Fearing she might be running late, Fluttershy quickly trotted off in search of Pinkie Pie. Fate had it that they both had the same day off, so they decided to meet for lunch. It wouldn't be anything extravagant. Rationing kept the ponies' meals from being too exciting. But Fluttershy was eager to see her friend again after so long.

Pinkie Pie had been the only one of her friends to stay in Ponyville after the war began. Fluttershy and Rainbow Dash were both forcibly conscripted into the Aerial Guard while Rarity and Twilight Sparkle were drafted into the Magical Guard. When Big McIntosh was drafted, Applejack had volunteered for service on the Front Line so that she could serve with her brother. Pinkie Pie was left in Ponyville, working at Mr. and Mrs. Cake's bakery, which had been contracted by the Palace to provide rationed bread to the whole community. She also helped out at the Apple Family Farm as often as she could; with both their hardest workers gone in the war effort, they were having a hard time keeping up with the demand for food.

Fluttershy found Pinkie Pie in the center of the Ponyville encampment where they both had been living for the past six months. Pinkie Pie was jumping up and down with excitement, which made Fluttershy smile. One of the reasons she had been looking forward to their meeting was that moment: she knew it all it would take was one smile from Pinkie Pie's face and all of her stress about the war would melt away.

"Fluttershy!" Pinkie Pie yelled, still bouncing. "I'm so excited!"

"I'm happy to see you too," Fluttershy replied softly. "How have you been?"

"Great!" Pinkie Pie said, smiling. "Let's go get some food. I'm _starving!_"

They made the short walk over to the mess tent. After they had their lunch rations, they found a couple seats in the corner of the tent where they wouldn't be bothered too much.

"How have you been?" Pinkie Pie asked enthusiastically as she ate her salad.

"I've been doing well," Fluttershy lied. She was not enjoying herself at all. But she didn't want to burden Pinkie Pie. "How about you?"

"I've been doing well too!" Pinkie Pie said between bites. "We've finally found the perfect way to cook bread in the new stone oven last month, so it's been going really well now!"

"That's wonderful," Fluttershy commented. She paused before asking, "Have you heard anything from the others?"

Pinkie Pie nodded. Fluttershy knew that if any pony would know, it would be Pinkie Pie. "I just saw Rarity last week!"

"Really?" Fluttershy asked with surprise. "Where is she working?"

"In the Manehattan encampment a few miles from here," Pinkie Pie replied. "She's helping with making the uniforms and saddle bags and stuff like that for the ponies on the Front Line! She's been helping to improve the uniforms too!"

"Wow," Fluttershy breathed. She hadn't seen Rarity in over a year. For a while, they were both stationed in Manehattan, but Fluttershy was transferred back to Ponyville around six months before the evacuation. She hadn't seen Rarity since her transfer. "Have you heard from anyone else?"

Pinkie nodded again, the pink curls of her mane bouncing happily as she did so. "Twilight Sparkle is going to be here in a couple weeks!"

"What for?"

"I heard she has some new defense techniques she developed that she's going to teach to the Ponyville Magical Guard," Pinkie Pie said as she swallowed the last of her salad. "She's doing a lot to try and help the Magical Guardsponies who are on the Front Line."

"Hopefully we'll get to see her when she comes here," Fluttershy said quietly. "I haven't been able to see her since in almost two years."

They spent the rest of their lunch talking about more pleasant things. When they parted ways, Fluttershy started for the edge of their encampment. Carefully, she waited for the gap in the Watch before slipping out into the forest. Quietly, she made her way to the tree line. It took an hour or more, but she eventually reached the edge of the forest. Relieved to have made it without any trouble, she looked out at the field in front of her. It was empty, save for the few Buffalo camps near the tree line. Beyond them, she could see the Front Line. The magic used for defense left the area hazy. And the Pegasus ponies had been sending rain clouds to the enemy's side of the Front since the start of the war, so it was always easy to tell how close they were. You just had to look for the rainclouds. In the last few months, however, the clouds were starting to get too close for Fluttershy's comfort.

"Welcome, Fluttershy," Chief Thunderhooves greeted in his low, booming voice as he walked over to the tree line from the nearest Buffalo camp. He was very imposing; his presence still made Fluttershy quiver a little.

"Good afternoon, Chief Thunderhooves," she replied quietly, still looking out at the horizon.

"The violence is worsening of late," the Chief commented. "We fear the Front Line may not last for long."

Fluttershy did not respond.

"Winter is coming," he continued, his voice somewhat despondent. "We may not be able to last a winter that arrives this early.

"The Pegasi are making the winter come early this year," Fluttershy informed him. "Princess Celestia asked us to."

Chief Thunderhooves snorted. "Is she wise to ask such a thing?"

"I don't know," Fluttershy said, mostly to herself. The Princess had requested the winter come early because during the previous winter, the cold weather had been a big boon to the ponies' war efforts. The invaders came from a hot, arid climate. They were cold-blooded, so the cold weather did not agree with them. It had forced their temporary retreat during the previous winter. Fluttershy doubted they would be so lucky this winter.

Lizards and Chameleons and Geckos. Just the thought of their scale-covered skin made her mane bristle. They had come to Equestria from Reptilia. They didn't seem like a big threat in the beginning, but the ponies soon regretted underestimating the invaders. Their siege against Equestria had been brutal. The ponies held out for eighteen months before they were forced to retreat into the Evertree Forest. After six months in forest encampments, spirits were low, and hope was all but gone.

An explosion sounded loudly in the distance. Fluttershy squinted her eyes at the bright flash of magic that followed.

"The shields are beginning to fail," Fluttershy whispered.

Chief Thunderhooves snorted again. "Let us hope for all our sakes that winter comes quickly."

* * *

Thank you for reading the first chapter of this story~! ^^ I hope you enjoyed it! Please leave a review if you feel so inclined. I always found it annoying that there are never any long-term villains on My Little Pony: Friendship is Magic. (At least, not in the first two seasons that I've watched on Netflix...) The second chapter is coming soon.


	2. Chapter 2

**Equestria Invaded**

* * *

"What was _that_?" Rainbow Dash yelled as she hovered in place, trying to regain her sight after being blinded by the bright flash a few hundred yards to her left. "Report!"

A Pegasus pony came flying over from the area of the disruption. "They broke through! They broke a small hole in the Shield!"

Rainbow Dash swore under her breath. "How many got through?"

"Maybe a dozen Chameleons," the pony reported. "The Unicorns sent reinforcements; it's closing up already. But they lost sight of the enemy almost immediately."

Rainbow dash felt like screaming in frustration. She quickly flew to the command center, which was located on a cloud a half mile or so from the Front Line. "Princess Luna," Rainbow Dash called, nearly crashing into the Princess as she landed. "I've just received a report that a dozen or more Chameleons broke through the Front Line."

Princess Luna's expression darkened. "I will lead the team that follows them. You gather three more of your fastest flyers and follow me."

Rainbow Dash nodded and quickly rounded up the fastest fliers she could think of that were nearby: Sassaflash, Lightning Dust, and Cloudchaser. The four Pegasi met up with Princess Luna as they began the search for the enemy party.

"I spoke with the ponies closest to the flash. They told me that the Chameleons headed this way," the Princess informed them as she gestured towards a group of trees. "Their camouflage doesn't work well in open spaces. They are likely hiding in the forest. As soon as we find them, we have to chase them out into the open. A team of Unicorns from the Magical Guard is going to meet us here, but they could take as long as fifteen minutes to arrive. We must find the Chameleons before they arrive."

The Pegasi nodded. When they reached the small group of trees, they began their search. They systematically began making sweeps close to the tops of the trees. Because of the autumn weather, the leaves were changing and fell from the trees easily as the Pegasi made their low passes. Suddenly, Rainbow Dash saw something. She silently caught the others' attention and gestured at the center of the trees. The leaves were rustling even though there were no ponies flying there. The Pegasi quickly brought a raincloud over and used the lightning to start the center of the forest on fire. In a few short minutes, the Chameleons were fleeing the flames, leaving the trees for the open fields that surrounded them. The Princess quickly caught the Chameleons in a magical shield and struggled to hold all twelve while they waited for the Unicorns to arrive and take them away. While Cloudchaser used the rain from the raincloud to put out the flames, Rainbow Dash and Lightning Dust flew circles around the entrapped Chameleons. Rainbow Dash shuddered as she eyed the reptiles. The way they could move their eyes independent of one another caused the short hair of her mane to bristle. Even though they had been caught, they were still trying to camouflage themselves. Rainbow Dash laughed bitterly.

Once the Chameleons had been taken away by the Unicorns to the prison camp, Princess Luna dismissed the Pegasi back to the Front Line. As they started to head back, she called for Rainbow Dash to stay behind.

"Rainbow Dash," the Princess began, "I need you to bring news of this to Princess Celestia."

Rainbow Dash nodded. "I'm on it."

"As fast as possible."

Rainbow Dash was gone the second the Princess stopped speaking. It took her a nearly an hour of flying, but eventually she reached the tree line. Exhausted, she landed and waited for an escort into the forest. Security was tight, and for good reason. She eyed the Buffalo camps as she entered the Evertree Forest. _I hope the Front Line doesn't get pushed back this far_, she thought, feeling sympathy for the Buffalos. They had enough trouble when it was just settler ponies taking their land. After this new threat, they had lost all of their traditional stomping grounds.

The sun was setting when Rainbow Dash reached the Canterlot encampment. Princess Celestia was waiting for her. Rainbow Dash bowed before telling the Princess the news. Princess Celestia's expression fell. She stood, looking contemplative for a moment before thanking Rainbow Dash for bringing her word so quickly. As Rainbow Dash was about to leave, Princess Celestia stopped her.

"I need you to stay here for at least a day," the Princess explained. "Twilight Sparkle is coming tomorrow to explain a new defensive technique she has developed and I would like your input."

"Wouldn't some other pony's opinion be more useful?" Rainbow Dash asked. She was anxious to rejoin the rest of her team on the Front Line.

Princess Celestia shook her head. "I want your opinion." She paused, seeing Rainbow Dash's expression. "Don't worry. You could probably use a day's rest. I will send word to the Front Line that I have detained you. For now, you should settle in for the night. It can be a little dangerous here in the Evertree Forest after dark."

Rainbow Dash nodded reluctantly. She was lead to a small tent near the Princess' tent and quickly removed her uniform and fell asleep. She didn't want to admit it to herself, and especially not to any pony else, but she was grateful for the opportunity to have some real sleep. She hadn't had a whole day of rest in over two months.

The next morning, Rainbow Dash was awake and ready shortly after dawn. She wandered around the Canterlot encampment impatiently, unsure what to do until Twilight Sparkle's presentation that afternoon. _I could always stop by and see how the Ponyville Aerial Guard are doing_. It didn't take long to fly over to the Ponyville encampment. The Aerial Guardsponies were delighted to see her, and the attention did wonders to lift Rainbow Dash's mood. When she took a fly around to see how the ponies on duty were faring, she was surprised to run into Fluttershy.

Fluttershy certainly looked different than Rainbow Dash remembered. Her hair was tightly braided, and her expression serious and alert. She obviously took her position as seriously as she should. Rainbow Dash nodded to Fluttershy, who nodded back. Her expression grew bright, and she was obviously trying not to smile. Rainbow Dash made a mental note to stop by and pay her friend a quick visit on her way back to the Front Line.

The time for the presentation finally arrived, and Rainbow Dash nodded and smiled at Twilight Sparkle when she entered the Princess' tent, where the presentation was taking place.

Twilight began speaking after a few brief words from the Princess. "As I'm sure you have all heard, we had a breach in the defensive magical shield along the Front Line yesterday." Twilight paused as the ponies murmured their agreement. "It has always been my fear that eventually the reptiles would find a way around the spell we use to power the Shield. A shield has never been in effect for so long, so we were unsure of the ramifications. It seems it is losing strength." Twilight paused again, letting her words sink in. Rainbow Dash silently wished she'd just get to the point. "I have been searching and searching for a way to strengthen the Shield, and I believe I've found a way." Twilight proceeded to pull out a board with a bunch of words and equations that Rainbow Dash didn't read. "I've found a spell that I believe will let us turn Pegasus wing power into power for the Shield." Rainbow Dash was finally intrigued. Sure, the Pegasus ponies were invaluable for message-sending and patrolling and early alerts of incoming danger, but she had always wished she could contribute in the same way the Unicorns of the Magical Guard could. "With this spell, we would be able to transform energy of the wing power produced by the Pegasi directly into magical energy that would strengthen the Shield. On a smaller scale, this spell would even allow a few Pegasi to form a shield without the help of a Unicorn, just with their wing power." The ponies gathered in the tent were thoroughly impressed, as was Rainbow Dash. This would be a huge help on the Front Line.

As soon as she was able, Rainbow Dash asked Princess Celestia if she could return to the Front Line right away so that they could begin preparations for the implementation of the new spell. The Princess told her she could return as soon as she liked, but that the Front Line was not expecting her back until the next morning, when Twilight Sparkle would be arriving with several Magical Guardsponies to assist her in implementing the spell.

Faced with the opportunity of having a bit of extra time on her hooves, Rainbow Dash decided to go find Fluttershy before she left the forest. It didn't take too long—all of the Guardsponies tents were located in the same area of the Ponyville encampment.

Fluttershy was surprised to see Rainbow Dash again, and insisted they go together to say a quick hello to Pinkie Pie before curfew started.

"Rainbow Dash!" Pinkie screamed, giving her friend a bigger hug than she would have probably liked. "How are you?"

"Not too great," Rainbow Dash replied truthfully. "I have to get back to the Front Line soon. The breach in the Shield has really thrown us for a loop."

"It'll be okay!" Pinkie Pie replied cheerily. "I'm sure you'll find a way to fix it."

"I'm not too sure. Twilight's idea seems pretty good, but we won't know until it's implemented and tested whether it will help us or not."

"I bet it wi~ill!" Pinkie Pie said in her sing-song-y way.

"But what if it doesn't?" Rainbow Dash yelled, causing both Fluttershy and Pinkie Pie to cower. "We have literally no idea if it will work or not! And there are a lot of ponies' lives at stake if it doesn't! Do you even have any idea how serious the situation is out there?" Rainbow Dash could feel herself taking the focus of her argument too wide, but it was too late to stop. "There are ponies dying every day while you are here singing away like it's not even happening!"

"Do you think I really don't know that?" Pinkie Pie asked, tears welling up in her eyes. "I know how dangerous it is for you and the other ponies. I know that ponies are dying every day to keep me safe. But if I don't keep smiling, I don't know what I would do…" Pinkie Pie started to cry. Fluttershy did her best to comfort her friend, but she was crying too.

"Pinkie Pie's smiles are the only thing that has kept me going these past few months," Fluttershy admitted quietly between sobs. "It's very selfish of you to try and take that away." The two ponies walked off, leaving a stunned Rainbow Dash to regret her actions as she flew back to the Front Line.

* * *

Thank you for reading this chapter! I hope it won't be over a month again before Chapter 3! ^^;; Please feel free to leave a review if you feel so inclined. I know this chapter ended on a kind of sad note~. The next chapter will focus on what's become of Rarity...


End file.
